Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation

Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals

The SILVER locus has been mapped in the domestic cat, identifying a unique genomic location distinct from that of any known reported gene associated with silver or hypopigmentation in mammals. A demonstrated lack of linkage to SILV, the strong candidate gene for silver, led to the initiation of a genome scan utilizing 2 pedigrees segregating for silver coat color. Linkage mapping defined a genomic region for SILVER as a 3.3-Mb region, (95.87-99.21 Mb) on chromosome D2, (peak logarithm of the odds = 10.5, = 0), which displays conserved synteny to a genomic interval between 118.58 and 121.85 Mb on chromosome 10 in the human genome. In the domestic cat, mutations at the SILVER locus suppress the development of pigment in the hair, but in contrast to other mammalian silver variants, there is an apparently greater influence on the production of pheomelanin than eumelanin pigment. The mapping of a novel locus for SILVER offers much promise in identifying a gene that may help elucidate aspects of pheomelanogenesis, a pathway that has been very elusive, and illustrates the promise of the cat genome project in increasing our understanding of basic biological processes of general relevance for mammals.

Oculocutaneous albinism in Suncus murinus: establishment of a strain and identification of its responsible gene

The house musk shrew Suncus murinus (Insectivora, Soricidae) is referred to as suncus in a laboratory context. Although the capture of albino-like shrews (wild suncus) has been reported previously, albino-like strains have never been established, and the molecular basis of the character has remained elusive. We have established an OCAO mutant strain (oculocutaneous albinism Okinawa), from a wild suncus with a white coat and red eyes, which was captured in 2002. During the course of establishing the strain, it was revealed that the albino-like phenotype was inherited in an autosomal recessive manner. To elucidate the molecular basis of this phenotype, we cloned the suncus cDNAs for tyrosinase (Tyr), pink-eyed dilution (p), and solute carrier family 45, member 2 (Slc45a2), since these genes are involved in oculocutaneous albinism in various species, including humans. Several polymorphisms were identified in these genes; however, linkage analysis excluded the involvement of Tyr and p. On the other hand, two amino acid substitutions (V240A and G366E) were identified in Slc45a2 that cosegregated with the phenotype in the OCAO mutant strain. While V240A was also present in colored suncus collected from Okinawa, G366E was unique to the albino-like suncus and heterozygous carriers. Thus, we conclude that a mutation in Slc45a2 (G366E) is responsible for an albino-like phenotype in Suncus murinus.

A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti

A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9x whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9x-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.

Albinism in the American mink (Neovison vison) is associated with a tyrosinase nonsense mutation

Albino phenotypes are documented in various species including the American mink. In other species the albino phenotypes are associated with tyrosinase (TYR) gene mutations; therefore TYR was considered the candidate gene for albinism in mink. Four microsatellite markers were chosen in the predicted region of the TYR gene. Genotypes at the markers Mvi6025 and Mvi6034 were found to be associated with the albino phenotype within an extended half-sib family. A BAC clone containing Mvi6034 was mapped to chromosome 7q1.1-q1.3 by fluorescent in situ hybridization. Subsequent analysis of genomic TYR sequences from wild-type and albino mink samples identified a nonsense mutation in exon 1, which converts a TGT codon encoding cysteine to a TGA stop codon (c.138T>A, p.C46X; EU627590). The mutation truncates more than 90% of the normal gene product including the putative catalytic domains. The results indicate that the nonsense mutation is responsible for the albino phenotype in the American mink.

State of cat genomics

Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

Initial sequence and comparative analysis of the cat genome

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.

Mapping of the Recessive White Locus and Analysis of the Tyrosinase Gene in Chickens

An F(2) chicken population of 265 individuals, obtained from an intercross between the Japanese Game (colored plumage) and the White Plymouth Rock (the recessive white) and genotyped for microsatellite markers, was used for determining the locus of the gene responsible for the recessive white plumage phenotype in chickens. Two hundred twenty-five markers were mapped in 28 linkage groups. Linkage analysis revealed that the recessive white gene was mapped to chromosome 1. Detailed analysis using additional markers uncovered a significant linkage between 2 new markers, mapped to the flanking region of the tyrosinase gene, which is associated with skin and plumage color. The sequence of the tyrosinase gene was investigated in recessive white chickens and colored chickens. There were no obvious differences in the tyrosinase gene exons between the recessive white chicken and the colored chicken. However, sequence analysis of tyrosinase intron 4 in the recessive white chicken revealed a presence of an insertion of an avian retroviral sequence. The White Plymouth Rock and the F(2) generation with white plumage were identified as homozygous carriers of the retroviral sequence. Expression of the normal transcript containing exon 5 was substantially decreased in the recessive white chicken compared with the colored chicken. Some abnormal tyrosinase gene transcripts were expressed in the skin of the White Plymouth Rock: reverse transcription PCR products amplified from exon 3 to intron 4 and from retroviral sequence 3' long terminal repeat to exon 5. Based on these results, it was confirmed that an avian retroviral sequence insertion in the tyrosinase gene was the cause of recessive white phenotype in chickens.

Identification of a tyrosinase (TYR) exon 4 deletion in albino ferrets (Mustela putorius furo)

Albinism is due to a lack of pigmentation in hair, skin and eye, and has been shown to occur in several animal species. Mutations of the tyrosinase (TYR) gene account for albinism in domestic cats, rabbits, cattle, mice and rats. In this study, we demonstrate that a TYR mutation accounts for albinism in the ferret (Mustela putorius furo). The coding sequence of the five exons of TYR was determined in genomic DNA from wild-type pigmented 'sable' coloured and albino ferrets. It was not possible to amplify TYR exon 4 in albino ferrets originating from different breeds. The deletion of exon 4 in albino ferrets was confirmed by Southern blot hybridization of genomic DNA from albino and pigmented ferrets. This is the first report of a deletion of a TYR exon in a non-human mammal.

Pigmentation in Black-boned sheep (Ovis aries): association with polymorphism of the Tyrosinase gene

Measurements were made in Black-boned (n = 40) and normal (n = 23) sheep (Ovis aries) from a flock in Nanping County of Yunnan Province, China, as well as a group (n = 21) of Romney Marsh sheep (O. aries) with the view to explaining the basis of the dark pigmentation occurring in the Black-boned animals. Plasma colour was significantly darker (P < 0.01) in Black-boned sheep than in their normal flock mates, which in turn had significantly darker plasma (P < 0.01) than the Romney Marsh sheep. Similar significant (P < 0.01) differences were measured for plasma tyrosinase activity and both groups of sheep from Nanping County had similar plasma concentrations of glutathione which were significantly smaller (P < 0.01) than for the Romney Marsh sheep.A partial fragment of 750 bp of exon 1 of the gene encoding tyrosinase was constructed and found to contain two silent mutation sites (G192C and C462T) but there was no effect on amino acid sequences of tyrosinase. Using restriction fragment length polymorphism analyses two allelic variants of site G192C were identified giving rise to the genotypes GG, GC and CC; the frequencies of allele G being 0.914, 0.824 and 0.286 in the Black-boned sheep, their flock mates and the Romney Marsh sheep respectively. Plasma tyrosinase activity was similar for genotypes GG and GC and for both genotypes significantly higher (P < 0.05) than for genotype CC. The sheep from Nanping County displayed only the GG and GC genotypes and had predominantly black or black and white coat colour whereas the Romney Marsh sheep were of either genotype GC or CC and exhibited only white coat colouration. It is not appears that the dark pigmentation of the Black-boned sheep arises because of polymorphisms in the exon 1 of tyrosinase gene. However, this result could explain the differences between Black-boned and Romney Marsh sheep but not for differences between Black-boned and Nanping Normal sheep. Moreover, this result has provided evidence of genetic markers in the form of polymorphisms of the tyrosinase gene which may help to find the black traits causing mutations. There would be merit in further studies using histochemical and molecular techniques to elucidate the causes of the dark pigmentation in these Black-boned sheep.

The genetics of cream coat color in dogs

Cream dogs of several breeds require a genotype of e/e at MC1R based on 27 individuals in this study. All Akita, Caucasian Mountain Dogs, German Shepherd Dogs, Miniature Schnauzer, and Puli with this genotype are cream, suggesting they are fixed at a second locus which causes the phaeomelanin pigmentation caused by this genotype to be diluted or pale. Conversely, although all Chinese Shar-Pei and Poodles that were cream had an e/e genotype at MC1R, not all dogs with this genotype are cream. Today, many Golden Retrievers and Labrador Retrievers with an e/e genotype are cream instead of the traditional yellow to golden color seen in the past. The second gene in these breeds must have multiple alleles, only one of which causes phaeomelanin pigment to be diluted or pale. Tyrosinase (TYR) and solute carrier family 45, member 2 (SLC45A2) have been shown to cause cream coat color in other species and were therefore investigated in dogs as candidate genes for this second locus. Although polymorphisms were detected in cDNA sequence from TYR and SLC45A2, no polymorphism was consistently associated with cream dogs or cosegregated with cream coat color in any of the families used in this study. A microsatellite was detected in a published BAC sequence (GenBank no. AAEX01017083) in intron 2 and was used to map SLC45A2 to CFA4.

A sex-linked allele, autosomal modifiers and temperature-dependence appear to regulate melanism in male mosquitofish (Gambusia holbrooki)

About 1% of male mosquitofish (Gambusia holbrooki) express melanic (mottled-black) body coloration, which differs dramatically from the wild-type, silvery-gray coloration. Here, I report on the genetic inheritance pattern of melanic coloration, which indicates Y-linkage, and at least one autosomal modifier. Phenotypic expression of melanism is also affected by temperature. Expression is constitutive (temperature insensitive) in some populations, inducible (temperature sensitive) in others. Constitutive and inducible expression occur among geographically proximal populations. However, males from any single population demonstrate the same constitutive or inducible expression pattern as one another. The F1 males from inter-population crosses demonstrate temperature-related expression patterns like their sires'. As well, the sex ratio of melanic males' progeny differs among populations. Here, inter-population crosses demonstrate a sex-ratio bias in the same direction as intra-population crosses of the sire population. About 20% of the male progeny of melanic sires express the wild-type phenotype. These silver F1 males sire only silver offspring, suggestive of loss of the melanin gene in F1 males from crossover between sex chromosomes, or control by additional modifiers, or involvement of additional factors. In nature, melanic males persist at very low frequencies. The data collected here on heritability indicate that genetic factors contribute to the rarity of melanic male mosquitofish.

A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes

We report the construction of a 1.5-Mb-resolution radiation hybrid map of the domestic cat genome. This new map includes novel microsatellite loci and markers derived from the 2X genome sequence that target previous gaps in the feline-human comparative map. Ninety-six percent of the 1793 cat markers we mapped have identifiable orthologues in the canine and human genome sequences. The updated autosomal and X-chromosome comparative maps identify 152 cat-human and 134 cat-dog homologous synteny blocks. Comparative analysis shows the marked change in chromosomal evolution in the canid lineage relative to the felid lineage since divergence from their carnivoran ancestor. The canid lineage has a 30-fold difference in the number of interchromosomal rearrangements relative to felids, while the felid lineage has primarily undergone intrachromosomal rearrangements. We have also refined the pseudoautosomal region and boundary in the cat and show that it is markedly longer than those of human or mouse. This improved RH comparative map provides a useful tool to facilitate positional cloning studies in the feline model.